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Articles by Moritz E. Beber
pyOpenSci/pyos-package-template: v0.6.11 Simplify hatch enviroments
Published April 7, 2026 | Version v0.6.11 Software Open What's Changed fix: small bug in building envt remove detached by @lwasser in https://github.com/pyOpenSci/pyos-package-template/pull/149 Full Changelog: https://github.com/pyOpenSci/pyos-package-template/compare/v0.6.10...v0.6.11 Software: https://github.com/pyOpenSci/pyos-package-template/tree/v0.6.11 (URL)
pyOpenSci/pyos-package-template: Add dependency groups to template and simplify
Published April 7, 2026 | Version v0.6.10 Software Open What's Changed feat(feature-groups): add feature group support to template and simplify by @lwasser in https://github.com/pyOpenSci/pyos-package-template/pull/148 Full Changelog: https://github.com/pyOpenSci/pyos-package-template/compare/v0.6.9...v0.6.10 Software: https://github.com/pyOpenSci/pyos-package-template/tree/v0.6.10 (URL)
pyOpenSci/pyos-package-template: v0.6.9 Release :sparkles:
Published November 5, 2025 | Version v0.6.9 Software Open What's Changed fix: trigger publish only on release by @lwasser in https://github.com/pyOpenSci/pyos-package-template/pull/140 release v0.6.9 by @lwasser in https://github.com/pyOpenSci/pyos-package-template/pull/141 Full Changelog: https://github.com/pyOpenSci/pyos-package-template/compare/v0.6.8...v0.6.9 Software: https://github.com/pyOpenSci/pyos-package-template/tree/v0.6.9 (URL)
pyOpenSci/pyos-package-template: vo.6.8 packaging template: Clean up and fix CI builds
Published November 5, 2025 | Version v0.6.8 Software Open This update makes the CI infra simpler that we provide. it splits each sit type into a separate job (test suite, linting, etc) It also cleans up some of the steps that weren't working as created.
pyOpenSci/pyos-package-template: v0.6.7 Release
Published November 3, 2025 | Version v0.6.7 Software Open [v0.6.7] Fix RTD build for Sphinx and move docs dependencies to optional-dependencies (@lwasser, #126, #130, #131) Remove typing annotations in FULL template mode (@lwasser, #134) Make test_audit script that doesn't fail (@erik-whiting, #120) Remove readthedocs.io URL from pyproject.toml for minimal version (@Michael-Howes, #119) Move all dependencies to optional-dependencies and use hatch features (@lwasser, #132) bug: ensure sphinx...
github.com/nf-core/funcscan
Published October 4, 2025 | Version 3.0.0 Software Open No description specified https://dockstore.org/aliases/workflow-versions/10.5281-zenodo.17267740 (URL) https://dockstore.org/workflows/github.com/nf-core/funcscan:3.0.0 (URL) https://dockstore.org/api/ga4gh/trs/v2/tools/%23workflow%2Fgithub.com%2Fnf-core%2Ffuncscan/versions/3.0.0/PLAIN-NFL/descriptor/nextflow.config (URL)
pyOpenSci/pyos-package-template: Release v0.6.5
Published July 4, 2025 | Version v0.6.5 Software Open I think I made up a new patch.patch version previously :) This adds UV as the default installer for Hatch environments.
pyOpenSci/pyos-package-template: v0.6.6 Release
Description Is it possible to have too many releases in a day? This is another patch to ensure UV is triggered to run hatch envs. What's Changed enh: development instructions for hatch envt by @lwasser in https://github.com/pyOpenSci/pyos-package-template/pull/115 Add: uv by @lwasser in https://github.com/pyOpenSci/pyos-package-template/pull/116 Full Changelog: https://github.com/pyOpenSci/pyos-package-template/compare/v0.6.5...v0.6.6
pyOpenSci/pyos-package-template: Release 0.6.4.1
Published July 3, 2025 | Version v0.6.4.1 Software Open A tiny patch that updates the readme and the first question to be more user-friendly. What's Changed enh: coc and readme update by @lwasser in https://github.com/pyOpenSci/pyos-package-template/pull/111 Full Changelog: https://github.com/pyOpenSci/pyos-package-template/compare/v0.6.4...v0.6.4.1 Software: https://github.com/pyOpenSci/pyos-package-template/tree/v0.6.4.1 (URL)
pyOpenSci/pyos-package-template: Release v0.6.4
This updates the copier workflow to make it more user-friendly. It also removes some extra items from the "minimal version" of the package.
pyOpenSci/pyos-package-template: Release v0.6.3
Published July 2, 2025 | Version v0.6.3 Software Open This release adds a more customized workflow with 3 main branches: minimal, full with defaults and full but select options you want to use! What's Changed Restore tests, fix #88 by @sneakers-the-rat in https://github.com/pyOpenSci/pyos-package-template/pull/92 Fix: contributing guide for template has typos by @lwasser in https://github.com/pyOpenSci/pyos-package-template/pull/93 Fix: typos in the contributing template by @lwasser in...
pyOpenSci/pyos-package-template: v0.6.2 release: add docs and tests to minimal build
What's Changed docs: add sneakers-the-rat as a contributor for code, and review by @allcontributors in https://github.com/pyOpenSci/pyos-package-template/pull/66 docs: add ucodery as a contributor for code, and review by @allcontributors in https://github.com/pyOpenSci/pyos-package-template/pull/68 docs: add lwasser as a contributor for code, and review by @allcontributors in https://github.com/pyOpenSci/pyos-package-template/pull/69 Add: zenodo badge to repo by @lwasser in...
github.com/nf-core/taxprofiler
Published March 13, 2025 | Version 1.2.3 Software Open No description specified https://dockstore.org/aliases/workflow-versions/10.5281-zenodo.15016755 (URL) https://dockstore.org/workflows/github.com/nf-core/taxprofiler:1.2.3 (URL) https://dockstore.org/api/ga4gh/trs/v2/tools/%23workflow%2Fgithub.com%2Fnf-core%2Ftaxprofiler/versions/1.2.3/PLAIN-NFL/descriptor/nextflow.config (URL)
pyOpenSci/pyos-package-template: v0.6.1 pyos package template
Published November 7, 2024 | Version v0.6.1 Software Open What's Changed docs: add Midnighter as a contributor for code, review, and ideas by @allcontributors in https://github.com/pyOpenSci/pyos-package-template/pull/45 docs: add blink1073 as a contributor for code, review, and ideas by @allcontributors in https://github.com/pyOpenSci/pyos-package-template/pull/46 Enable concurrent tests by @Midnighter in https://github.com/pyOpenSci/pyos-package-template/pull/55 Support multi-line...
nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling
Abstract Metagenomic classification tackles the problem of characterising the taxonomic source of all DNA sequencing reads in a sample. A common approach to address the differences and biases between the many different taxonomic classification tools is to run metagenomic data through multiple classification tools and databases.
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
Correction to: Nature Biotechnology https://doi.org/10.1038/s41587-020-0446-y, published online 2 March 2020. This paper was originally published under standard Springer Nature copyright (© The Author(s), under exclusive licence to Springer Nature America, Inc.). It is now available as an open-access paper under a Creative Commons Attribution 4.0 International license. The error has been corrected in the HTML and PDF versions of the article.
MEMOTE for standardized genome-scale metabolic model testing
Fig. 1: Graphical summary of MEMOTE. Fig. 2: Quality of manually reconstructed GEMs from collections without quality control or quality assurance. Data availability The model collection is available at https://doi.org/10.5281/zenodo.2636858. Individual results and aggregated tables, as well as analysis code, are available at https://doi.org/10.5281/zenodo.2638234.
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